SessionReader.cpp 85.4 KB
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///////////////////////////////////////////////////////////////////////////////
//
// File SessionReader.cpp
//
// For more information, please see: http://www.nektar.info
//
// The MIT License
//
// Copyright (c) 2006 Division of Applied Mathematics, Brown University (USA),
// Department of Aeronautics, Imperial College London (UK), and Scientific
// Computing and Imaging Institute, University of Utah (USA).
//
// License for the specific language governing rights and limitations under
// Permission is hereby granted, free of charge, to any person obtaining a
// copy of this software and associated documentation files (the "Software"),
// to deal in the Software without restriction, including without limitation
// the rights to use, copy, modify, merge, publish, distribute, sublicense,
// and/or sell copies of the Software, and to permit persons to whom the
// Software is furnished to do so, subject to the following conditions:
//
// The above copyright notice and this permission notice shall be included
// in all copies or substantial portions of the Software.
//
// THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS
// OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
// FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL
// THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
// LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
// FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER
// DEALINGS IN THE SOFTWARE.
//
// Description: Session reader
//
///////////////////////////////////////////////////////////////////////////////

#ifndef TIXML_USE_STL
#define TIXML_USE_STL
#endif

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#include <LibUtilities/BasicUtils/SessionReader.h>

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#include <iostream>
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#include <fstream>
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#include <string>
using namespace std;

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#include <boost/iostreams/filtering_streambuf.hpp>
#include <boost/iostreams/copy.hpp>
#include <boost/iostreams/filter/gzip.hpp>
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#include <boost/algorithm/string.hpp>
#include <tinyxml/tinyxml.h>
#include <LibUtilities/BasicUtils/ErrorUtil.hpp>
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#include <LibUtilities/BasicUtils/Equation.h>
#include <LibUtilities/Memory/NekMemoryManager.hpp>
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#include <LibUtilities/BasicUtils/MeshPartition.h>
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#include <LibUtilities/BasicUtils/ParseUtils.hpp>
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#include <LibUtilities/BasicUtils/FileSystem.h>
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#include <boost/program_options.hpp>
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#include <boost/format.hpp>
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namespace po = boost::program_options;
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namespace io = boost::iostreams;
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namespace Nektar
{
    namespace LibUtilities
    {
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        /**
         * @class SessionReader
         *
         * This class provides an interface to Nektar++-specific content in a
         * supplied XML document. It also initialises a Nektar++ session
         * including setting up communication for parallel execution and where
         * necessary partitioning the supplied mesh for running across multiple
         * processes.
         *
         * A session should be initialised at the beginning of a user's
         * application by passing the command-line arguments. This not only
         * allows the SessionReader to extract the name of the XML document to
         * load containing Nektar++ session information, but also supplies the
         * MPI arguments necessary for setting up parallel communication. The
         * SessionReader should be initialised using the #CreateInstance
         * function:
         * @code
         * LibUtilities::SessionReaderSharedPtr vSession
         *          = LibUtilities::SessionReader::CreateInstance(argc, argv);
         * @endcode
         * The instance \c vSession can now be passed to other key Nektar++
         * components during their construction.
         * @note At the end of the user application, it is important to call the
         * #Finalise routine in order to finalise any MPI communication and
         * correctly free resources.
         *
         * The SessionReader class provides streamlined, validated access to
         * session parameters, solver information and functions defined within a
         * Nektar++ XML document. The available routines and their usage is
         * documented below.
         *
         * In the case of solver information properties, the classes to which
         * these parameters are pertinent may register with the SessionReader
         * class the set of valid values for a given property. Such values may
         * also be associated with an enumeration value for more transparent use
         * of the property values in code.
         */

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        /**
         * This map of maps stores the list of valid string values for a number
         * of solver information parameters. The top level map connects
         * different parameter names to their list of possible values. The list
         * of possible values is also a map, mapping a valid string to a
         * corresponding enum value.
         *
         * This list is populated through the #RegisterEnumValue static member
         * function which is called statically from various classes to register
         * the valid values for solver info parameters associated with them. The
         * map is therefore fully populated before the SessionReader class is
         * instantiated and a file is read in and parsed.
         */
        EnumMapList SessionReader::m_enums;


        /**
         * List of default values for solver information parameters to be used
         * in the case of them not being provided.
         *
         * This list is populated through the #RegisterDefaultSolverInfo static
         * member variable which is called statically from various classes to
         * register the default value for a given parameter.
         */
        SolverInfoMap SessionReader::m_solverInfoDefaults;


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        /**
         * List of values for GlobalSysSoln parameters to be used to override
         * details given in SolverInfo
         *
         * This list is populated by ReadGlobalSysSoln if the
         * GLOBALSYSSOLNINFO section is defined in the input file.
         * This List allows for details to define for the Global Sys
         * solver for each variable. 
         */
        GloSysSolnInfoList SessionReader::m_gloSysSolnList;

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        /**
         * Lists the possible command-line argument which can be specified for
         * this executable.
         *
         * This list is populated through the #RegisterCmdLineArgument static
         * member function which is called statically from various classes to
         * register command-line arguments they need.
         */
        CmdLineArgMap SessionReader::m_cmdLineArguments;


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        /**
         * This constructor parses the command-line arguments given to the user
         * application to set up any MPI communication, read supplied XML
         * session files, and partition meshes where necessary.
         *
         * @param   argc        Number of command-line arguments
         * @param   argv        Array of command-line arguments
         */
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        SessionReader::SessionReader(int argc, char *argv[])
        {
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            m_xmlDoc    = 0;
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            m_filenames = ParseCommandLineArguments(argc, argv);
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            ASSERTL0(m_filenames.size() > 0, "No session file(s) given.");
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            m_filename    = m_filenames[0];
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            m_sessionName = m_filename.substr(0, m_filename.find_last_of('.'));
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            if (m_filename.size() > 3 &&
                m_filename.substr(m_filename.size() - 3, 3) == ".gz")
            {
                m_sessionName =
                    m_sessionName.substr(0, m_sessionName.find_last_of('.'));
            }
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            // Create communicator
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            CreateComm(argc, argv);
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            // If running in parallel change the default global sys solution
            // type.
            if (m_comm->GetSize() > 1)
            {
                m_solverInfoDefaults["GLOBALSYSSOLN"] = 
                    "IterativeStaticCond";
            }
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        }


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        /**
         *
         */
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        SessionReader::SessionReader(
            int                             argc, 
            char                           *argv[], 
            const std::vector<std::string> &pFilenames, 
            const CommSharedPtr            &pComm)
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        {
            ASSERTL0(pFilenames.size() > 0, "No filenames specified.");

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            ParseCommandLineArguments(argc, argv);
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            m_xmlDoc      = 0;
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            m_filenames   = pFilenames;
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            m_filename    = pFilenames[0];
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            m_sessionName = m_filename.substr(0, m_filename.find_last_of('.'));
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            if (m_filename.size() > 3 &&
                m_filename.substr(m_filename.size() - 3, 3) == ".gz")
            {
                m_sessionName =
                    m_sessionName.substr(0, m_sessionName.find_last_of('.'));
            }
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            // Create communicator
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            if (!pComm.get())
            {
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                CreateComm(argc, argv);
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            }
            else
            {
                m_comm = pComm;
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                if (m_comm->GetSize() > 1)
                {
                    m_solverInfoDefaults["GLOBALSYSSOLN"] = 
                        "IterativeStaticCond";
                }
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            }
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            // If running in parallel change the default global sys solution
            // type.
            if (m_comm->GetSize() > 1)
            {
                m_solverInfoDefaults["GLOBALSYSSOLN"] = 
                    "IterativeStaticCond";
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            }
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        }


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        /**
         *
         */
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        SessionReader::~SessionReader()
        {
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            delete m_xmlDoc;
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        }

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        /**
         * Performs the main initialisation of the object. The XML file provided
         * on the command-line is loaded and any mesh partitioning is done. The
         * resulting process-specific XML file (containing the process's
         * geometry partition) is then reloaded and parsed.
         */
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        void SessionReader::InitSession()
        {
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            m_exprEvaluator.SetRandomSeed((m_comm->GetRank() + 1) * time(NULL));

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            // Split up the communicator
            PartitionComm();

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            // Partition mesh
            PartitionMesh();

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            // Parse the XML data in #m_xmlDoc
            ParseDocument();
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            // Override SOLVERINFO and parameters with any specified on the
            // command line.
            CmdLineOverride();
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        }

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        /**
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         * @brief Parses the command-line arguments for known options and
         * filenames.
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         */
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        std::vector<std::string> SessionReader::ParseCommandLineArguments(
            int argc, char *argv[])
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        {
            // List the publically visible options (listed using --help)
            po::options_description desc("Allowed options");
            desc.add_options()
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                ("verbose,v",    "be verbose")
                ("help,h",       "print this help message")
                ("solverinfo,I", po::value<vector<std::string> >(), 
                                 "override a SOLVERINFO property")
                ("parameter,P",  po::value<vector<std::string> >(),
                                 "override a parameter")
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                ("shared-filesystem,s", "Using shared filesystem.")
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                ("npx",          po::value<int>(),
                                 "number of procs in X-dir")
                ("npy",          po::value<int>(),
                                 "number of procs in Y-dir")
                ("npz",          po::value<int>(),
                                 "number of procs in Z-dir")
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                ("part-only",    po::value<int>(),
                                 "only partition mesh into N partitions.")
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                ("part-info",    "Output partition information")
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            ;
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            CmdLineArgMap::const_iterator cmdIt;
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            for (cmdIt  = m_cmdLineArguments.begin(); 
                 cmdIt != m_cmdLineArguments.end(); ++cmdIt)
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            {
                std::string names = cmdIt->first;
                if (cmdIt->second.shortName != "")
                {
                    names += "," + cmdIt->second.shortName;
                }
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                if (cmdIt->second.isFlag)
                {
                    desc.add_options()
                        (names.c_str(), cmdIt->second.description.c_str())
                    ;
                }
                else
                {
                    desc.add_options()
                        (names.c_str(), po::value<std::string>(),
                         cmdIt->second.description.c_str())
                    ;
                }
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            }
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            // List hidden options (e.g. session file arguments are not actually
            // specified using the input-file option by the user).
            po::options_description hidden("Hidden options");
            hidden.add_options()
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                    ("input-file", po::value< vector<string> >(), 
                                   "input filename")
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            ;

            // Combine all options for the parser
            po::options_description all("All options");
            all.add(desc).add(hidden);

            // Session file is a positional option
            po::positional_options_description p;
            p.add("input-file", -1);

            // Parse the command-line options
            po::parsed_options parsed = po::command_line_parser(argc, argv).
                                                options(all).
                                                positional(p).
                                                allow_unregistered().
                                                run();

            // Extract known options to map and update
            po::store(parsed, m_cmdLineOptions);
            po::notify(m_cmdLineOptions);

            // Help message
            if (m_cmdLineOptions.count("help"))
            {
                cout << desc << endl;
                exit(0);
            }

            // Enable verbose mode
            if (m_cmdLineOptions.count("verbose"))
            {
                m_verbose = true;
            }
            else
            {
                m_verbose = false;
            }
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            // Print a warning for unknown options
            std::vector< po::basic_option<char> >::iterator x;
            for (x = parsed.options.begin(); x != parsed.options.end(); ++x)
            {
                if (x->unregistered)
                {
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                    cout << "Warning: Unknown option: " << x->string_key 
                         << endl;
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                }
            }

            // Return the vector of filename(s) given as positional options
            if (m_cmdLineOptions.count("input-file"))
            {
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                return m_cmdLineOptions["input-file"].as<
                    std::vector<std::string> >();
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            }
            else
            {
                return std::vector<std::string>();
            }
        }


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        /**
         *
         */
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        TiXmlDocument& SessionReader::GetDocument()
        {
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            ASSERTL1(m_xmlDoc, "XML Document not defined.");
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            return *m_xmlDoc;
        }

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        /**
         * The single parameter specifies a path to the requested element in a
         * similar format to the filesystem path. Given the following XML:
         * @code
         * <NEKTAR>
         *   <CONDITIONS>
         *     <PARAMETERS>
         *     ...
         *     </PARAMETERS>
         *   </CONDITIONS>
         * </NEKTAR>
         * @endcode
         * the PARAMETERS element would be retrieved by requesting the path:
         * @code
         * Nektar/Conditions/Parameters
         * @endcode
         * @note Paths are case-insensitive.
         *
         * @param   pPath       Path to requested element.
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         *
         * @return Direct pointer to requested XML Element.
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         */
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        TiXmlElement* SessionReader::GetElement(const string& pPath)
        {
            std::string vPath = boost::to_upper_copy(pPath);
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            std::vector<std::string> st;
            boost::split(st, vPath, boost::is_any_of("\\/ "));
            ASSERTL0(st.size() > 0, "No path given in XML element request.");
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            TiXmlElement* vReturn = m_xmlDoc->FirstChildElement(st[0].c_str());
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            ASSERTL0(vReturn, std::string("Cannot find element '")
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                              + st[0] + std::string("'."));
            for (int i = 1; i < st.size(); ++i)
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            {
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                vReturn = vReturn->FirstChildElement(st[i].c_str());
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                ASSERTL0(vReturn, std::string("Cannot find element '")
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                                  + st[i] + std::string("'."));
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            }
            return vReturn;
        }

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        /**
         *
         */
        bool SessionReader::DefinesElement(const std::string &pPath) const
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        {
            std::string vPath = boost::to_upper_copy(pPath);
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            std::vector<std::string> st;
            boost::split(st, vPath, boost::is_any_of("\\/ "));
            ASSERTL0(st.size() > 0, "No path given in XML element request.");
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            TiXmlElement* vReturn = m_xmlDoc->FirstChildElement(st[0].c_str());
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            ASSERTL0(vReturn, std::string("Cannot find element '")
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                              + st[0] + std::string("'."));
            for (int i = 1; i < st.size(); ++i)
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            {
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                vReturn = vReturn->FirstChildElement(st[i].c_str());
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                if (!vReturn) return false;
            }
            return true;
        }

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        /**
         *
         */
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        const std::string& SessionReader::GetFilename() const
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        {
            return m_filename;
        }

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        /**
         *
         */
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        const std::string& SessionReader::GetSessionName() const
        {
            return m_sessionName;
        }

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        /**
         * Output is of the form [sessionName]_P[idx] where idx is the rank
         * of the process.
         */
        const std::string SessionReader::GetSessionNameRank() const
        {
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            std::string  dirname = m_sessionName + "_xml"; 
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            fs::path     pdirname(dirname);
            
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            std::string vFilename = "P" + boost::lexical_cast<std::string>(m_comm->GetRowComm()->GetRank());
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            fs::path    pFilename(vFilename);            
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            fs::path fullpath = pdirname / pFilename;
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            return PortablePath(fullpath);
        }
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        /**
         *
         */
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        CommSharedPtr& SessionReader::GetComm()
        {
            return m_comm;
        }

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        /**
         * This routine finalises any parallel communication.
         *
         * @note This routine should be called at the very end of a users
         * application.
         */
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        void SessionReader::Finalise()
        {
            m_comm->Finalise();
        }

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        /**
         *
         */
        bool SessionReader::DefinesParameter(const std::string& pName) const
        {
            std::string vName = boost::to_upper_copy(pName);
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            ParameterMap::const_iterator paramIter = m_parameters.find(vName);
            return (paramIter != m_parameters.end());
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        }

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        /**
         * If the parameter is not defined, termination occurs. Therefore, the
         * parameters existence should be tested for using #DefinesParameter
         * before calling this function.
         *
         * @param   pName       The name of a floating-point parameter.
         * @returns The value of the floating-point parameter.
         */
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        const NekDouble& SessionReader::GetParameter(
            const std::string& pName) const
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        {
            std::string vName = boost::to_upper_copy(pName);
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            ParameterMap::const_iterator paramIter = m_parameters.find(vName);
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            ASSERTL0(paramIter != m_parameters.end(),
                     "Unable to find requested parameter: " + pName);
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            return paramIter->second;
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        }

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        /**
         *
         */
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        void SessionReader::LoadParameter(
            const std::string &pName, int &pVar) const
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        {
            std::string vName = boost::to_upper_copy(pName);
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            ParameterMap::const_iterator paramIter = m_parameters.find(vName);
            ASSERTL0(paramIter != m_parameters.end(), "Required parameter '" + 
                     pName + "' not specified in session.");
            pVar = (int)floor(paramIter->second);
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        }

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        /**
         *
         */
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        void SessionReader::LoadParameter(
            const std::string &pName, int &pVar, const int &pDefault) const
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        {
            std::string vName = boost::to_upper_copy(pName);
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            ParameterMap::const_iterator paramIter = m_parameters.find(vName);
            if(paramIter != m_parameters.end())
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            {
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                pVar = (int)floor(paramIter->second);
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            }
            else
            {
                pVar  = pDefault;
            }
        }

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        /**
         *
         */
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        void SessionReader::LoadParameter(
            const std::string &pName, NekDouble& pVar) const
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        {
            std::string vName = boost::to_upper_copy(pName);
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            ParameterMap::const_iterator paramIter = m_parameters.find(vName);
            ASSERTL0(paramIter != m_parameters.end(), "Required parameter '" + 
                     pName + "' not specified in session.");
            pVar = paramIter->second;
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        }

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        /**
         *
         */
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        void SessionReader::LoadParameter(
            const std::string &pName, 
                  NekDouble   &pVar, 
            const NekDouble   &pDefault) const
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        {
            std::string vName = boost::to_upper_copy(pName);
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            ParameterMap::const_iterator paramIter = m_parameters.find(vName);
            if(paramIter != m_parameters.end())
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            {
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                pVar = paramIter->second;
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            }
            else
            {
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                pVar = pDefault;
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            }
        }

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        /**
         *
         */
        void SessionReader::SetParameter(const std::string &pName, int &pVar) 
        {
            std::string vName = boost::to_upper_copy(pName);
            m_parameters[vName] = pVar;
        }


        /**
         *
         */
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        void SessionReader::SetParameter(
            const std::string &pName, NekDouble& pVar) 
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        {
            std::string vName = boost::to_upper_copy(pName);
            m_parameters[vName] = pVar;
        }



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        /**
         *
         */
        bool SessionReader::DefinesSolverInfo(const std::string &pName) const
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        {
            std::string vName = boost::to_upper_copy(pName);
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            SolverInfoMap::const_iterator infoIter = m_solverInfo.find(vName);
            return (infoIter != m_solverInfo.end());
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        }

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        /**
         *
         */
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        const std::string& SessionReader::GetSolverInfo(
            const std::string &pProperty) const
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        {
            std::string vProperty = boost::to_upper_copy(pProperty);
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            SolverInfoMap::const_iterator iter = m_solverInfo.find(vProperty);
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            ASSERTL1(iter != m_solverInfo.end(),
                     "Unable to find requested property: " + pProperty);
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            return iter->second;
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        }

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        /**
         *
         */
        void SessionReader::SetSolverInfo(
            const std::string &pProperty, const std::string &pValue) 
        {
            std::string vProperty = boost::to_upper_copy(pProperty);
            SolverInfoMap::iterator iter = m_solverInfo.find(vProperty);

            ASSERTL1(iter != m_solverInfo.end(),
                     "Unable to find requested property: " + pProperty);

            iter->second = pValue;
        }
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        /**
         *
         */
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        void SessionReader::LoadSolverInfo(
            const std::string &pName, 
                  std::string &pVar, 
            const std::string &pDefault) const
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        {
            std::string vName = boost::to_upper_copy(pName);
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            SolverInfoMap::const_iterator infoIter = m_solverInfo.find(vName);
            if(infoIter != m_solverInfo.end())
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            {
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                pVar = infoIter->second;
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            }
            else
            {
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                pVar = pDefault;
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            }
        }

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        /**
         *
         */
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        void SessionReader::MatchSolverInfo(
            const std::string &pName,
            const std::string &pTrueVal,
                  bool        &pVar,
            const bool        &pDefault) const
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        {
            std::string vName = boost::to_upper_copy(pName);
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            SolverInfoMap::const_iterator infoIter = m_solverInfo.find(vName);
            if(infoIter != m_solverInfo.end())
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            {
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                pVar = boost::iequals(infoIter->second, pTrueVal);
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            }
            else
            {
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                pVar = pDefault;
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            }
        }

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        /**
         *
         */
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        bool SessionReader::MatchSolverInfo(
            const std::string &pName,
            const std::string &pTrueVal) const
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        {
            if (DefinesSolverInfo(pName))
            {
                std::string vName = boost::to_upper_copy(pName);
744 745
                SolverInfoMap::const_iterator iter = m_solverInfo.find(vName);
                if(iter != m_solverInfo.end())
746 747 748 749 750 751 752 753
                {
                    return true;
                }
            }
            return false;
        }


754 755 756 757 758 759 760 761 762 763 764 765 766 767 768 769 770 771 772 773 774 775 776 777 778 779 780 781 782 783 784 785 786 787 788 789 790 791 792 793 794 795 796 797
        /**
         *
         */
        bool SessionReader::DefinesGlobalSysSolnInfo(const std::string &pVariable, 
                                                     const std::string &pProperty) const
        {

            GloSysSolnInfoList::const_iterator iter = m_gloSysSolnList.find(pVariable);
            if(iter == m_gloSysSolnList.end())
            {
                return false;
            }

            std::string vProperty = boost::to_upper_copy(pProperty);
            
            GloSysInfoMap::const_iterator iter1 = iter->second.find(vProperty);
            if(iter1 == iter->second.end())
            {
                return false;
            }
            
            return true;
        }

        
        /**
         *
         */
        const std::string &SessionReader::GetGlobalSysSolnInfo(const std::string &pVariable, const std::string &pProperty) const
        {
            GloSysSolnInfoList::const_iterator iter; 

            ASSERTL0( (iter = m_gloSysSolnList.find(pVariable)) != m_gloSysSolnList.end(),
                      "Failed to find variable in GlobalSysSolnInfoList");

            std::string vProperty = boost::to_upper_copy(pProperty);
            GloSysInfoMap::const_iterator iter1; 

            ASSERTL0( (iter1 = iter->second.find(vProperty)) != iter->second.end(),
                      "Failed to find property: " + vProperty + " in GlobalSysSolnInfoList");
            
            return iter1->second;
        }
        
798 799 800 801
        /**
         *
         */
        bool SessionReader::DefinesGeometricInfo(const std::string &pName) const
802 803
        {
            std::string vName = boost::to_upper_copy(pName);
804 805
            GeometricInfoMap::const_iterator iter = m_geometricInfo.find(vName);
            return (iter != m_geometricInfo.end());
806 807
        }

808 809 810 811

        /**
         *
         */
812 813 814 815
        void SessionReader::LoadGeometricInfo(
            const std::string &pName,
                  std::string &pVar,
            const std::string &pDefault) const
816 817
        {
            std::string vName = boost::to_upper_copy(pName);
818 819
            GeometricInfoMap::const_iterator iter = m_geometricInfo.find(vName);
            if(iter != m_geometricInfo.end())
820
            {
821
                pVar = iter->second;
822 823 824
            }
            else
            {
825
                pVar = pDefault;
826 827 828
            }
        }

829 830 831 832

        /**
         *
         */
833 834 835 836
        void SessionReader::LoadGeometricInfo(
            const std::string &pName,
                  bool        &pVar,
            const bool        &pDefault) const
837 838
        {
            std::string vName = boost::to_upper_copy(pName);
839 840
            GeometricInfoMap::const_iterator iter = m_geometricInfo.find(vName);
            if(iter != m_geometricInfo.end())
841
            {
842
                if (iter->second == "TRUE")
843 844 845 846 847 848 849 850 851 852
                {
                    pVar = true;
                }
                else
                {
                    pVar = false;
                }
            }
            else
            {
853
                pVar = pDefault;
854 855 856
            }
        }

857

858 859 860
        /**
         *
         */
861 862 863 864
        void SessionReader::LoadGeometricInfo(
            const std::string &pName,
                  NekDouble   &pVar,
            const NekDouble   &pDefault) const
865 866
        {
            std::string vName = boost::to_upper_copy(pName);
867 868
            GeometricInfoMap::const_iterator iter = m_geometricInfo.find(vName);
            if(iter != m_geometricInfo.end())
869
            {
870
                pVar = std::atoi(iter->second.c_str());
871 872 873
            }
            else
            {
874
                pVar = pDefault;
875 876 877 878
            }
        }


879 880 881
        /**
         *
         */
882 883 884 885 886
        void SessionReader::MatchGeometricInfo(
            const std::string &pName,
            const std::string &pTrueVal,
                  bool        &pVar,
            const bool        &pDefault) const
887 888
        {
            std::string vName = boost::to_upper_copy(pName);
889 890
            GeometricInfoMap::const_iterator iter = m_geometricInfo.find(vName);
            if(iter != m_geometricInfo.end())
891
            {
892
                pVar = boost::iequals(iter->second, pTrueVal);
893 894 895 896 897 898 899 900
            }
            else
            {
                pVar  = pDefault;
            }
        }


901 902 903
        /**
         *
         */
904 905
        const std::string& SessionReader::GetVariable(
            const unsigned int &idx) const
906 907 908 909 910
        {
            ASSERTL0(idx < m_variables.size(), "Variable index out of range.");
            return m_variables[idx];
        }

911

912 913 914 915 916 917 918 919 920 921 922 923

        /**
         *
         */
        void SessionReader::SetVariable(const unsigned int &idx, 
                                        std::string newname) 
        {
            ASSERTL0(idx < m_variables.size(), "Variable index out of range.");
            m_variables[idx] = newname;
        }


924 925 926
        /**
         *
         */
927 928 929 930 931
        std::vector<std::string> SessionReader::GetVariables() const
        {
            return m_variables;
        }

932 933 934 935 936 937 938 939 940 941 942 943 944 945 946 947 948 949 950 951

        /**
         *
         */
        bool SessionReader::DefinesFunction(const std::string &pName) const
        {
            FunctionMap::const_iterator it1;
            std::string vName = boost::to_upper_copy(pName);

            if ((it1 = m_functions.find(vName)) != m_functions.end())
            {
                return true;
            }
            return false;
        }


        /**
         *
         */
952 953
        bool SessionReader::DefinesFunction(
            const std::string &pName,
954 955
            const std::string &pVariable,
            const int pDomain) const
956 957
        {
            FunctionMap::const_iterator it1;
958
            FunctionVariableMap::const_iterator it2;
959 960
            std::string vName = boost::to_upper_copy(pName);

961 962
            // Check function exists
            if ((it1 = m_functions.find(vName))     != m_functions.end())
963
            {
964 965
                pair<std::string, int> key(pVariable,pDomain);
                pair<std::string, int> defkey("*",pDomain);
966
                bool varExists =
967 968
                    (it2 = it1->second.find(key)) != it1->second.end() ||
                    (it2 = it1->second.find(defkey)) != it1->second.end();
969
                return varExists;
970 971 972 973 974 975 976 977
            }
            return false;
        }


        /**
         *
         */
978 979
        EquationSharedPtr SessionReader::GetFunction(
            const std::string &pName,
980 981
            const std::string &pVariable,
            const int pDomain) const
982 983
        {
            FunctionMap::const_iterator it1;
984
            FunctionVariableMap::const_iterator it2, it3;
985 986 987 988 989
            std::string vName = boost::to_upper_copy(pName);

            ASSERTL0((it1 = m_functions.find(vName)) != m_functions.end(),
                     std::string("No such function '") + pName
                     + std::string("' has been defined in the session file."));
990 991

            // Check for specific and wildcard definitions
992 993 994 995 996 997
            pair<std::string,int> key(pVariable,pDomain);
            pair<std::string,int> defkey("*",pDomain);
            bool specific = (it2 = it1->second.find(key)) !=
                it1->second.end();
            bool wildcard = (it3 = it1->second.find(defkey)) !=
                it1->second.end();
998 999 1000

            // Check function is defined somewhere
            ASSERTL0(specific || wildcard,
1001 1002 1003 1004
                     "No such variable " + pVariable
                     + " in domain " + boost::lexical_cast<string>(pDomain) 
                     + " defined for function " + pName
                     + " in session file.");
1005 1006 1007 1008 1009 1010 1011

            // If not specific, must be wildcard
            if (!specific)
            {
                it2 = it3;
            }

1012
            ASSERTL0((it2->second.m_type == eFunctionTypeExpression),
1013
                    std::string("Function is defined by a file."));
1014
            return it2->second.m_expression;
1015 1016
        }

1017 1018 1019 1020

        /**
         *
         */
1021 1022
        EquationSharedPtr SessionReader::GetFunction(
            const std::string  &pName,
1023 1024
            const unsigned int &pVar,
            const int pDomain) const
1025 1026
        {
            ASSERTL0(pVar < m_variables.size(), "Variable index out of range.");
1027
            return GetFunction(pName, m_variables[pVar],pDomain);
1028 1029
        }

1030 1031 1032 1033

        /**
         *
         */
1034 1035
        enum FunctionType SessionReader::GetFunctionType(
            const std::string &pName,
1036 1037
            const std::string &pVariable,
            const int pDomain) const
1038 1039
        {
            FunctionMap::const_iterator it1;
1040
            FunctionVariableMap::const_iterator it2, it3;
1041 1042 1043 1044 1045 1046
            std::string vName = boost::to_upper_copy(pName);

            it1 = m_functions.find(vName);
            ASSERTL0 (it1 != m_functions.end(),
                      std::string("Function '") + pName
                      + std::string("' not found."));
1047 1048

            // Check for specific and wildcard definitions
1049 1050 1051
            pair<std::string,int> key(pVariable,pDomain);
            pair<std::string,int> defkey("*",pDomain);
            bool specific = (it2 = it1->second.find(key)) !=
1052
                            it1->second.end();
1053
            bool wildcard = (it3 = it1->second.find(defkey)) !=
1054 1055 1056 1057
                            it1->second.end();

            // Check function is defined somewhere
            ASSERTL0(specific || wildcard,
1058 1059 1060 1061
                     "No such variable " + pVariable
                     + " in domain " + boost::lexical_cast<string>(pDomain) 
                     + " defined for function " + pName
                     + " in session file.");
1062 1063 1064 1065 1066 1067 1068

            // If not specific, must be wildcard
            if (!specific)
            {
                it2 = it3;
            }

1069
            return it2->second.m_type;
1070 1071
        }

1072 1073 1074 1075

        /**
         *
         */
1076 1077
        enum FunctionType SessionReader::GetFunctionType(
            const std::string  &pName,
1078 1079
            const unsigned int &pVar,
            const int pDomain) const
1080 1081
        {
            ASSERTL0(pVar < m_variables.size(), "Variable index out of range.");
1082
            return GetFunctionType(pName, m_variables[pVar],pDomain);
1083 1084 1085 1086 1087 1088
        }


        /**
         *
         */
1089 1090
        std::string SessionReader::GetFunctionFilename(
            const std::string &pName, 
1091 1092
            const std::string &pVariable,
            const int pDomain) const
1093 1094
        {
            FunctionMap::const_iterator it1;
1095
            FunctionVariableMap::const_iterator it2, it3;
1096 1097 1098 1099 1100 1101
            std::string vName = boost::to_upper_copy(pName);

            it1 = m_functions.find(vName);
            ASSERTL0 (it1 != m_functions.end(),
                      std::string("Function '") + pName
                      + std::string("' not found."));
1102 1103

            // Check for specific and wildcard definitions
1104 1105 1106
            pair<std::string,int> key(pVariable,pDomain);
            pair<std::string,int> defkey("*",pDomain);
            bool specific = (it2 = it1->second.find(key)) !=
1107
                            it1->second.end();
1108
            bool wildcard = (it3 = it1->second.find(defkey)) !=
1109 1110 1111 1112
                            it1->second.end();

            // Check function is defined somewhere
            ASSERTL0(specific || wildcard,
1113 1114 1115 1116 1117
                     "No such variable " + pVariable
                     + " in domain " + boost::lexical_cast<string>(pDomain) 
                     + " defined for function " + pName
                     + " in session file.");
            
1118 1119 1120 1121 1122 1123
            // If not specific, must be wildcard
            if (!specific)
            {
                it2 = it3;
            }

1124 1125 1126 1127 1128 1129 1130
            return it2->second.m_filename;
        }


        /**
         *
         */
1131 1132
        std::string SessionReader::GetFunctionFilename(
            const std::string  &pName, 
1133 1134
            const unsigned int &pVar,
            const int pDomain) const
1135 1136
        {
            ASSERTL0(pVar < m_variables.size(), "Variable index out of range.");
1137
            return GetFunctionFilename(pName, m_variables[pVar],pDomain);
1138 1139 1140
        }


1141 1142 1143 1144 1145 1146 1147 1148 1149
        /**
         *
         */
        AnalyticExpressionEvaluator& SessionReader::GetExpressionEvaluator()
        {
            return m_exprEvaluator;
        }


1150 1151 1152 1153
        /**
         *
         */
        bool SessionReader::DefinesTag(const std::string &pName) const
1154 1155
        {
            std::string vName = boost::to_upper_copy(pName);
1156
            TagMap::const_iterator vTagIterator = m_tags.find(vName);
1157 1158 1159
            return (vTagIterator != m_tags.end());
        }

1160 1161 1162 1163

        /**
         *
         */
1164 1165 1166
        void SessionReader::SetTag(
            const std::string &pName, 
            const std::string &pValue)
1167 1168 1169 1170 1171
        {
            std::string vName = boost::to_upper_copy(pName);
            m_tags[vName] = pValue;
        }

1172 1173 1174 1175 1176

        /**
         *
         */
        const std::string &SessionReader::GetTag(const std::string& pName) const
1177 1178
        {
            std::string vName = boost::to_upper_copy(pName);
1179
            TagMap::const_iterator vTagIterator = m_tags.find(vName);
1180 1181 1182 1183 1184
            ASSERTL0(vTagIterator != m_tags.end(),
                     "Requested tag does not exist.");
            return vTagIterator->second;
        }

1185

1186 1187 1188 1189 1190 1191 1192 1193 1194
        /**
         *
         */
        const FilterMap &SessionReader::GetFilters() const
        {
            return m_filters;
        }


1195 1196 1197
        /**
         *
         */
1198 1199
        bool SessionReader::DefinesCmdLineArgument(
            const std::string& pName) const
1200 1201 1202 1203 1204
        {
            return (m_cmdLineOptions.find(pName) != m_cmdLineOptions.end());
        }


1205 1206 1207 1208 1209 1210
        /**
         *
         */
        void SessionReader::SubstituteExpressions(std::string& pExpr)
        {
            ExpressionMap::iterator exprIter;
1211 1212
            for (exprIter  = m_expressions.begin(); 
                 exprIter != m_expressions.end(); ++exprIter)
1213 1214 1215 1216 1217
            {
                boost::replace_all(pExpr, exprIter->first, exprIter->second);
            }
        }

1218 1219 1220 1221
        CompositeOrdering SessionReader::GetCompositeOrdering() const
        {
            return m_compOrder;
        }
1222

1223 1224 1225 1226 1227
        BndRegionOrdering SessionReader::GetBndRegionOrdering() const
        {
            return m_bndRegOrder;
        }

1228 1229 1230 1231 1232 1233 1234
        /**
         *
         */
        void SessionReader::LoadDoc(
            const std::string &pFilename,
            TiXmlDocument* pDoc) const
        {
1235 1236
            if (pFilename.size() > 3 &&
                pFilename.substr(pFilename.size() - 3, 3) == ".gz")
1237
            {
1238 1239 1240
                ifstream file(pFilename.c_str(),
                              ios_base::in | ios_base::binary);
                ASSERTL0(file.good(), "Unable to open file: " + pFilename);
1241
                stringstream ss;
1242 1243
                io::filtering_streambuf<io::input> in;
                in.push(io::gzip_decompressor());
1244
                in.push(file);
1245 1246 1247 1248 1249 1250 1251 1252 1253 1254
                try
                {
                    io::copy(in, ss);
                    ss >> (*pDoc);
                }
                catch (io::gzip_error& e)
                {
                    ASSERTL0(false,
                             "Error: File '" + pFilename + "' is corrupt.");
                }
1255
            }
1256 1257 1258 1259 1260 1261 1262 1263 1264 1265 1266 1267 1268
            else if (pFilename.size() > 4 &&
                    pFilename.substr(pFilename.size() - 4, 4) == "_xml")
            {
                fs::path    pdirname(pFilename);
                boost::format pad("P%1$07d.xml");
                pad % m_comm->GetRank();
                fs::path    pRankFilename(pad.str());
                fs::path fullpath = pdirname / pRankFilename;

                ifstream file(PortablePath(fullpath).c_str());
                ASSERTL0(file.good(), "Unable to open file: " + fullpath.string());
                file >> (*pDoc);
            }
1269 1270
            else
            {
1271 1272 1273
                ifstream file(pFilename.c_str());
                ASSERTL0(file.good(), "Unable to open file: " + pFilename);
                file >> (*pDoc);
1274 1275 1276
            }
        }

1277 1278 1279
        /**
         *
         */
1280 1281
        TiXmlDocument *SessionReader::MergeDoc(
            const std::vector<std::string> &pFilenames) const
1282
        {
1283 1284
            ASSERTL0(pFilenames.size() > 0, "No filenames for merging.");

1285
            // Read the first document
1286 1287 1288
            TiXmlDocument *vMainDoc = new TiXmlDocument;
            LoadDoc(pFilenames[0], vMainDoc);

1289
            TiXmlHandle vMainHandle(vMainDoc);
1290 1291
            TiXmlElement* vMainNektar = 
                vMainHandle.FirstChildElement("NEKTAR").Element();
1292 1293 1294 1295

            // Read all subsequent XML documents.
            // For each element within the NEKTAR tag, use it to replace the
            // version already present in the loaded XML data.
1296
            for (int i = 1; i < pFilenames.size(); ++i)
1297
            {
1298 1299
                if((pFilenames[i].compare(pFilenames[i].size()-3,3,"xml") == 0)
                   ||(pFilenames[i].compare(pFilenames[i].size()-6,6,"xml.gz") == 0))
1300
                {
1301 1302 1303 1304 1305 1306 1307 1308 1309 1310
                    TiXmlDocument* vTempDoc = new TiXmlDocument;
                    LoadDoc(pFilenames[i], vTempDoc);
                    
                    TiXmlHandle docHandle(vTempDoc);
                    TiXmlElement* vTempNektar;
                    vTempNektar = docHandle.FirstChildElement("NEKTAR").Element();
                    ASSERTL0(vTempNektar, "Unable to find NEKTAR tag in file.");
                    TiXmlElement* p = vTempNektar->FirstChildElement();
                    
                    while (p)
1311
                    {
1312 1313 1314 1315 1316 1317 1318 1319 1320
                        TiXmlElement *vMainEntry = 
                            vMainNektar->FirstChildElement(p->Value());
                        TiXmlElement *q = new TiXmlElement(*p);
                        if (vMainEntry)
                        {
                            vMainNektar->RemoveChild(vMainEntry);
                        }
                        vMainNektar->LinkEndChild(q);
                        p = p->NextSiblingElement();
1321
                    }